User: Johannes Rainer

gravatar for Johannes Rainer
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Italy
Twitter:
@jotsetung
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6 hours ago
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2 years, 6 months ago
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j**************@eurac.edu

PhD, Bioinformatics Group, Center for Biomedicine, EURAC Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 172 results • page 1 of 18 • next >
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Comment: C: Is mapId supposed to concatenate multiVals?
... that's right. Unfortunately I'm currently concatenating entrezgene identifiers for the same gene using a ; in the database. That might change in the future, or, when I find the time to redo the database layout. ...
written 7 days ago by Johannes Rainer760
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Yes, you can directly access it with the name - I would expect the ID to be sort of stable, but I'm not sure. > library(AnnotationHub) > edb <- AnnotationHub()[["AH53211"]] snapshotDate(): 2017-04-25 require(“ensembldb”) loading from cache '/Users/jo//.AnnotationHub/59949' > edb EnsDb ...
written 7 days ago by Johannes Rainer760
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Answer: A: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Looks like that error was reported elsewhere too: https://github.com/joey711/phyloseq/issues/717 Eventually re-install S4Vectors, ensembldb, AnnotationFilter might help. BiocInstaller::biocLite(c("S4Vectors", "ensembldb", "AnnotationFilter") type="source")   ...
written 7 days ago by Johannes Rainer760
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Looks like that error was reported elsewhere too: https://github.com/joey711/phyloseq/issues/717 Eventually re-install S4Vectors, ensembldb, AnnotationFilter might help. BiocInstaller::biocLite(c("S4Vectors", "ensembldb", "AnnotationFilter") type="source") ...
written 7 days ago by Johannes Rainer760
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... The standalone packages are "stable". But be aware that e.g. EnsDb.Hsapiens.v75 is built on Ensembl release 75, so it will never change and never updated! To get the human gene definitions from Ensembl release 86 you can: > library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 20 ...
written 7 days ago by Johannes Rainer760
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Answer: A: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Hi, can you please provide the output of sessionInfo()? I have no problem with the keys call. To get the Ensembl gene IDs out of an EnsDb object you can also: library(EnsDb.Hsapiens.v75) gene_ids <- genes(EnsDb.Hsapiens.v75, columns = "gene_id")$gene_id head(gene_ids) [1] "ENSG00000223972" "E ...
written 7 days ago by Johannes Rainer760
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Comment: C: mzR (2.8.1) Rcpp (0.12.10) compiler linker issue in Bioconductor 3.4, R 3.3.3
... And you should also use the devel xcms version. ...
written 5 weeks ago by Johannes Rainer760
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Comment: C: mzR (2.8.1) Rcpp (0.12.10) compiler linker issue in Bioconductor 3.4, R 3.3.3
... Also, if you want to use the new functionality described in https://www.bioconductor.org/packages/devel/bioc/vignettes/xcms/inst/doc/new_functionality.html you'll need the current developmental xcms version (1.51.10). The xcms from Bioconductor release 3.4 that you are using does not provide these f ...
written 5 weeks ago by Johannes Rainer760
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Answer: A: New to mass spec data analysis
... If you're starting with xcms I suggest you use the new xcms user interface which will be officially available with the upcoming Bioconductor release (version 3.5, will be released end of April). If you want to use it already now, you can try to get it from github (https://github.com/sneumann/xcms). ...
written 7 weeks ago by Johannes Rainer760
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Answer: A: Problem running dexseq in parallel using BiocParallel
... Hi, I've the same problems on my MacBook (since macos 10.12, eventually already earlier). My workaround for this is to use SnowParam instead of the MulticoreParam (along with setting options(bphost="localhost")). Sometimes MulticoreParam works but I didn't get to the point to understand what causes ...
written 7 weeks ago by Johannes Rainer760

Latest awards to Johannes Rainer

Student 6 days ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 6 weeks ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Problem running dexseq in parallel using BiocParallel
Scholar 6 weeks ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Scholar 13 months ago, created an answer that has been accepted. For A: Missing SYMBOL keytype in EnsDb.Hsapiens.v75
Scholar 13 months ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74
Scholar 13 months ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 13 months ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 13 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Popular Question 15 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Appreciated 16 months ago, created a post with more than 5 votes. For A: biomaRt no longer works with proxy after upgrade
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Centurion 17 months ago, created 100 posts.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 18 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 18 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Supporter 18 months ago, voted at least 25 times.
Scholar 18 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Autobiographer 23 months ago, has more than 80 characters in the information field of the user's profile.

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